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Q9SHE7

- RUB1_ARATH

UniProt

Q9SHE7 - RUB1_ARATH

Protein

Ubiquitin-NEDD8-like protein RUB1

Gene

RUB1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity.By similarity
    NEDD8-like protein RUB1: Appears to function as a stable post-translational protein modifier. An AMP-RUB1 intermediate is formed by an activating enzyme, distinct from the ubiquitin activating enzyme E1, which is composed of a heterodimer AXR1/ECR1. Auxin response is mediated, at least in part, through modification of the cullin AtCUL1 by the attachment of RUB1 to 'Lys-692'.2 Publications

    GO - Biological processi

    1. ethylene biosynthetic process Source: TAIR
    2. protein neddylation Source: TAIR
    3. response to auxin Source: TAIR

    Keywords - Biological processi

    Ubl conjugation pathway

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin-NEDD8-like protein RUB1
    Cleaved into the following 2 chains:
    Alternative name(s):
    Ubiquitin-related protein 1
    Short name:
    AtRUB1
    Gene namesi
    Name:RUB1
    Synonyms:NEDD8, UBQ15
    Ordered Locus Names:At1g31340
    ORF Names:T19E23.13
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 1

    Organism-specific databases

    TAIRiAT1G31340.

    Subcellular locationi

    Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

    GO - Cellular componenti

    1. cytosol Source: TAIR
    2. nucleus Source: UniProtKB-SubCell
    3. plasma membrane Source: TAIR

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 7676UbiquitinPRO_0000396910Add
    BLAST
    Chaini77 – 15276NEDD8-like protein RUB1PRO_0000035965Add
    BLAST
    Propeptidei153 – 1564CuratedPRO_0000035966

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation
    Cross-linki152 – 152Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    PaxDbiQ9SHE7.
    PRIDEiQ9SHE7.

    Expressioni

    Tissue specificityi

    Expressed in leaves, stems and flowers.1 Publication

    Gene expression databases

    GenevestigatoriQ9SHE7.

    Interactioni

    Subunit structurei

    NEDD8-like protein RUB1: Forms a thiol ester with the heterodimer AXR1/ECR1, specifically with the 'Cys-215' of ECR1.

    Protein-protein interaction databases

    BioGridi25258. 3 interactions.

    Structurei

    Secondary structure

    1
    156
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi78 – 825
    Beta strandi88 – 925
    Helixi99 – 11012
    Helixi114 – 1163
    Beta strandi117 – 1215
    Helixi133 – 1353
    Beta strandi142 – 1476

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BT0X-ray1.70A77-152[»]
    ProteinModelPortaliQ9SHE7.
    SMRiQ9SHE7. Positions 1-152.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9SHE7.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 7676Ubiquitin-like 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini77 – 15276Ubiquitin-like 2PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the ubiquitin family.Curated
    Contains 2 ubiquitin-like domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG5272.
    KOiK12158.
    OMAiKNSNKEQ.
    PhylomeDBiQ9SHE7.

    Family and domain databases

    InterProiIPR019956. Ubiquitin.
    IPR000626. Ubiquitin-like.
    IPR029071. Ubiquitin-rel_dom.
    IPR019954. Ubiquitin_CS.
    [Graphical view]
    PfamiPF00240. ubiquitin. 2 hits.
    [Graphical view]
    PRINTSiPR00348. UBIQUITIN.
    SMARTiSM00213. UBQ. 2 hits.
    [Graphical view]
    SUPFAMiSSF54236. SSF54236. 2 hits.
    PROSITEiPS00299. UBIQUITIN_1. 2 hits.
    PS50053. UBIQUITIN_2. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9SHE7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL    50
    EDGRTLADYN IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDTID 100
    RIKERVEEKE GIPPVQQRLI YAGKQLADDK TAKDYNIEGG SVLHLVLALR 150
    GGFGLL 156
    Length:156
    Mass (Da):17,397
    Last modified:August 10, 2010 - v3
    Checksum:iFA8D702BB9C1B3AE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC007654 Genomic DNA. Translation: AAF24594.1.
    CP002684 Genomic DNA. Translation: AEE31344.1.
    BT005749 mRNA. Translation: AAO64156.1.
    BT006110 mRNA. Translation: AAP04095.1.
    AK228591 mRNA. Translation: BAF00506.1.
    PIRiC86439.
    RefSeqiNP_564379.2. NM_102873.4.
    UniGeneiAt.25337.
    At.30783.
    At.43046.

    Genome annotation databases

    EnsemblPlantsiAT1G31340.1; AT1G31340.1; AT1G31340.
    GeneIDi840023.
    KEGGiath:AT1G31340.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC007654 Genomic DNA. Translation: AAF24594.1 .
    CP002684 Genomic DNA. Translation: AEE31344.1 .
    BT005749 mRNA. Translation: AAO64156.1 .
    BT006110 mRNA. Translation: AAP04095.1 .
    AK228591 mRNA. Translation: BAF00506.1 .
    PIRi C86439.
    RefSeqi NP_564379.2. NM_102873.4.
    UniGenei At.25337.
    At.30783.
    At.43046.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BT0 X-ray 1.70 A 77-152 [» ]
    ProteinModelPortali Q9SHE7.
    SMRi Q9SHE7. Positions 1-152.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 25258. 3 interactions.

    Proteomic databases

    PaxDbi Q9SHE7.
    PRIDEi Q9SHE7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G31340.1 ; AT1G31340.1 ; AT1G31340 .
    GeneIDi 840023.
    KEGGi ath:AT1G31340.

    Organism-specific databases

    TAIRi AT1G31340.

    Phylogenomic databases

    eggNOGi COG5272.
    KOi K12158.
    OMAi KNSNKEQ.
    PhylomeDBi Q9SHE7.

    Miscellaneous databases

    EvolutionaryTracei Q9SHE7.

    Gene expression databases

    Genevestigatori Q9SHE7.

    Family and domain databases

    InterProi IPR019956. Ubiquitin.
    IPR000626. Ubiquitin-like.
    IPR029071. Ubiquitin-rel_dom.
    IPR019954. Ubiquitin_CS.
    [Graphical view ]
    Pfami PF00240. ubiquitin. 2 hits.
    [Graphical view ]
    PRINTSi PR00348. UBIQUITIN.
    SMARTi SM00213. UBQ. 2 hits.
    [Graphical view ]
    SUPFAMi SSF54236. SSF54236. 2 hits.
    PROSITEi PS00299. UBIQUITIN_1. 2 hits.
    PS50053. UBIQUITIN_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "The ubiquitin-related protein RUB1 and auxin response in Arabidopsis."
      del Pozo J.C., Timpte C., Tan S., Callis J., Estelle M.
      Science 280:1760-1763(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH AXR1 AND ECR1.
    6. "The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein RUB1."
      del Pozo J.C., Estelle M.
      Proc. Natl. Acad. Sci. U.S.A. 96:15342-15347(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. "Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants."
      Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.
      Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-29; LYS-33; LYS-48 AND LYS-63.
      Strain: cv. Landsberg erecta.
    8. "The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis."
      Rao-Naik C., delaCruz W., Laplaza J.M., Tan S., Callis J., Fisher A.J.
      J. Biol. Chem. 273:34976-34982(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 79-152, TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiRUB1_ARATH
    AccessioniPrimary (citable) accession number: Q9SHE7
    Secondary accession number(s): O80715
    , P59263, Q0WQU3, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 31, 2003
    Last sequence update: August 10, 2010
    Last modified: October 1, 2014
    This is version 102 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to a ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3